0.10.1

A patch release fixing bugs stemming from 0.10.0.

What's Changed

🐛 Bug Fixes

• Write out correlations when --create-matrices doesn't include "all" by @tsalo in #1326
• Use confounds file with non-steady-state columns to identify dummy volumes by @tsalo in #1330

Other Changes

• Document the nichart mode by @tsalo in #1325
• Update indexed-gzip requirement from ~=1.8.7 to ~=1.9.1 by @dependabot in #1327

Full Changelog: 0.10.0...0.10.1

0.10.0

This backwards-incompatible release brings XCP-D further in line with the fMRIPost workflows in the NiPreps ecosystem.
We have added the ability to provide custom confound sets defined as YAML config files,
ingress derivatives from fMRIPost BIDS Apps (for example, fMRIPost-AROMA),
and provide external atlases organized as BIDS-Atlas datasets.

Please note that the BIDS-Atlas extension proposal has not been merged into BIDS yet,
so the expected organization of these external atlas datasets may change over time.

What's Changed

🛠 Breaking Changes

• Replace restricted confound sets with config files by @tsalo in #1255
• Rename --derivatives parameter to --datasets by @tsalo in #1276
• Accept external atlases by searching BIDS-Atlas datasets by @tsalo in #1265
• Move hemi entity before space by @tsalo in #1287

🎉 Exciting New Features

• Remove Freesurfer node from surface normalization workflow by @tsalo in #1273
• Track Sources with BIDSURI interface by @tsalo in #1283
• Add nichart mode by @tsalo in #1320

🐛 Bug Fixes

• Patch task_id into bids_filters by @tsalo in #1271
• Fix NIfTI-surface connection by @tsalo in #1284
• Update build image version by @tsalo in #1293
• Fix bug with surfaces and external atlases by @tsalo in #1304
• Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in #1300
• Fix ingression of standard-space mesh files by @tsalo in #1309
• Fix init_qc_report_wf connections when linc-qc and abcc-qc are disabled by @tsalo in #1314

Other Changes

• Don't rerun alff if num threads changes by @mattcieslak in #1263
• Remove xcp_d_dir and clean datasinks by @tsalo in #1262
• Add dataset links to config object by @tsalo in #1266
• Document minimal required inputs by @tsalo in #1270
• Correct documentation regarding Freesurfer by @tsalo in #1277
• Improve custom confound documentation by @tsalo in #1280
• Improve documentation of new features by @tsalo in #1281
• Use ruff for linting by @tsalo in #1312
• Fix links to documentation by @tsalo in #1323

Full Changelog: 0.9.1...0.10.0

0.10.0rc3

What's Changed

🐛 Bug Fixes

• Apply notch filter appropriate number of times based on --motion-filter-order by @tsalo in #1300
• Fix ingression of standard-space mesh files by @tsalo in #1309

Full Changelog: 0.10.0rc2...0.10.0rc3

0.10.0rc2

What's Changed

🛠 Breaking Changes

• Move hemi entity before space by @tsalo in #1287

🎉 Exciting New Features

• Track Sources with BIDSURI interface by @tsalo in #1283

🐛 Bug Fixes

• Fix NIfTI-surface connection by @tsalo in #1284
• Update build image version by @tsalo in #1293
• Fix bug with surfaces and external atlases by @tsalo in #1304

Other Changes

• Improve documentation of new features by @tsalo in #1281

Full Changelog: 0.10.0rc1...0.10.0rc2

0.10.0rc1

What's Changed

🛠 Breaking Changes

• Replace restricted confound sets with config files by @tsalo in #1255
• Rename --derivatives parameter to --datasets by @tsalo in #1276
• Accept external atlases by searching BIDS-Atlas datasets by @tsalo in #1265

🎉 Exciting New Features

• Remove Freesurfer node from surface normalization workflow by @tsalo in #1273

🐛 Bug Fixes

• Patch task_id into bids_filters by @tsalo in #1271

Other Changes

• Don't rerun alff if num threads changes by @mattcieslak in #1263
• Remove xcp_d_dir and clean datasinks by @tsalo in #1262
• Add dataset links to config object by @tsalo in #1266
• Document minimal required inputs by @tsalo in #1270
• Correct documentation regarding Freesurfer by @tsalo in #1277
• Improve custom confound documentation by @tsalo in #1280

Full Changelog: 0.9.1...0.10.0rc1

0.9.1

This release improves performance with multi-core processing.

What's Changed

Other Changes

• Remove n_procs for nodes that do not use multiple cores by @tsalo in #1256
• Remove unused data files by @tsalo in #1259
• Parallelize ALFF by @tsalo in #1258
• Replace internal data module with acres by @tsalo in #1260

Full Changelog: 0.9.0...0.9.1

0.9.0

This backwards-incompatible makes two important breaking changes. First, we changd the default file format for 'linc' mode from NIfTI to CIFTI. Second, XCP-D no longer ingresses and warps the anatomical tissue segmentation file (*_dseg.nii.gz), since no one was using it and it's easy enough to collect separately.

Additionally, this release fixes a bug with the collection of sphere files needed to warp fsnative surfaces to fsLR space, which should only affect derivatives from fMRIPrep and Nibabies versions >= 24.0.0 (i.e., versions that include space-fsnative in the spheres' filenames).

What's Changed

🛠 Breaking Changes

• Change linc mode default file format to CIFTI by @tsalo in #1248
• Stop ingressing anatomical-space tissue segmentation file by @tsalo in #1190

🎉 Exciting New Features

• Internally support voxel-wise confounds by @tsalo in #1244

🐛 Bug Fixes

• Fix subject sphere query by @tsalo in #1249

Full Changelog: 0.8.3...0.9.0

0.8.3

This patch release fixes a bug introduced in 0.8.1.

What's Changed

🐛 Bug Fixes

• Fix collection in case of derivatives with T1w and T2w but T1w is primary by @tsalo in #1240

Other Changes

• Document how to request a new mode by @tsalo in #1238

Full Changelog: 0.8.2...0.8.3

0.8.2

This release adds the "none" option for the mode parameter.

What's Changed

🎉 Exciting New Features

• Implement "none" mode by @tsalo in #1232

🐛 Bug Fixes

• Account for floating point issues in ALFF time array creation by @tsalo in #1236

Full Changelog: 0.8.1...0.8.2

0.8.1

Patch release for HBCD to support Nibabies runs with both T1w and T2w data.

What's Changed

🐛 Bug Fixes

• Explicitly check for -p none and --custom-confounds by @tsalo in #1222

Other Changes

• Restructure XCP-D to better match fMRIPrep by @tsalo in #1225
• Document the apptainer version requirements by @tsalo in #1233
• Make collect_data work for T1w+T2w nibabies derivatives by @tsalo in #1234

Full Changelog: 0.8.0...0.8.1